3O13 | pdb_00003o13

Crystal structure of a superantigen-like protein (SAV0433) from Staphylococcus aureus MU50 at 2.05 A resolution

PDB DOI: https://doi.org/10.2210/pdb3O13/pdb

Classification: TOXIN
Organism(s): Staphylococcus aureus subsp. aureus Mu50
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-07-20 Released: 2010-08-25
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.240 (Depositor), 0.250 (DCC)
R-Value Work:
0.191 (Depositor), 0.200 (DCC)
R-Value Observed:
0.193 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of a superantigen-like protein (SAV0433) from Staphylococcus aureus MU50 at 2.05 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 22.69 kDa
Atom Count: 1,641
Modeled Residue Count: 187
Deposited Residue Count: 198
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superantigen-like protein	A	198	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0 Gene Names: set15, SAV0433
UniProt
Find proteins for A0A0H3JXK4 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore A0A0H3JXK4 Go to UniProtKB: A0A0H3JXK4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H3JXK4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.240 (Depositor), 0.250 (DCC)
R-Value Work: 0.191 (Depositor), 0.200 (DCC)
R-Value Observed: 0.193 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33O13

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.161	α = 90
b = 90.804	β = 90
c = 109.129	γ = 90

Software Package:

Software Name	Purpose
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-08-25

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-08-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-07-20
Changes: Structure summary
Version 1.3: 2023-02-01
Changes: Database references, Derived calculations
Version 1.4: 2024-10-16
Changes: Data collection, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.